IUCrJ最新文献

{"title":"Cryo-EM-guided subtractive optimization of a novel VCP/p97 inhibitor","authors":"Jason Crawford,&nbsp;Ravi Munuganti,&nbsp;Charles Leung,&nbsp;Kriti Singh,&nbsp;Ellen Gates,&nbsp;Xing Zhu,&nbsp;Marcel Bally,&nbsp;Nancy Dos Santos,&nbsp;Maryam Sharifiaghdam,&nbsp;Zeynab Nosrati,&nbsp;Peter Axerio-Cilies,&nbsp;Alison M. Berezuk,&nbsp;Spencer Cholak,&nbsp;Alan Merk,&nbsp;Dale R. Cameron,&nbsp;Sriram Subramaniam","doi":"10.1107/S2052252526004604","DOIUrl":"10.1107/S2052252526004604","url":null,"abstract":"<div><div>We report the cryo-EM structure-guided discovery of GND-135, a novel small-mol­ecule inhibitor of the VCP/p97 AAA ATPase that demonstrates efficient inhibition of VCP/p97 in biochemical, cellular, and pharmacokinetic assays and in a tumor efficacy mouse model of acute myeloid leukemia. Our approach overcomes the liability in the clinical-stage com­pound CB-5083 where Phase I studies showed off-target activity of CB-5083 for the enzyme PDE6. From the cryo-EM structural analysis of CB-5083 bound to PDE6 and VCP/p97, we identified critical ligand/protein inter­actions in both proteins and rationally designed a small mol­ecule that retains key inter­actions necessary for VCP/p97 inhibition while eliminating PDE6 off-target activity. We refer to this approach as ‘subtractive optimization’ because we are leveraging our ability to determine both on-target and off-target cryo-EM structures to guide the medicinal chemistry campaign to enable more targeted com­pound design. While this strategy is not possible in all cases, the use of cryo-EM to tune on-site binding while eliminating off-target binding could be a generally applicable strategy for informing mol­ecular design and accelerating small-mol­ecule drug discovery.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 364-372"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148294634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural physiology of distinctive water channels elucidated by cryo-EM","authors":"Daisuke Kozai,&nbsp;Shota Suzuki,&nbsp;Akiko Kamegawa,&nbsp;Yoshinori Fujiyoshi","doi":"10.1107/S2052252526003234","DOIUrl":"10.1107/S2052252526003234","url":null,"abstract":"<div><div>Aqua­porins (AQPs) are membrane channel proteins that facilitate the transport of water and related solutes, playing indispensable roles across a wide range of organisms. Extensive structural studies using X-ray crystallography and electron crystallography have provided fundamental insights into the physiological functions of various AQPs. Recent advances in the structural analysis using single-particle cryo-electron microscopy, which bypasses the requirement for crystallization, have profoundly enhanced our understanding of AQP mechanisms. In this review, we summarize recent progress in AQP biology, providing a comparative analysis of orthodox, glycerol-permeable and unorthodox AQPs.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 312-323"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148054592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defect structure of yttria-stabilized hafnia nanoparticles","authors":"Magnus Nørgaard Kløve,&nbsp;Andreas Dueholm Bertelsen,&nbsp;Mads Ry Vogel Jørgensen,&nbsp;Bo Brummerstedt Iversen","doi":"10.1107/S2052252526003829","DOIUrl":"10.1107/S2052252526003829","url":null,"abstract":"<div><div>High-tem­per­a­ture polymorphs of hafnia (HfO₂) are of significant inter­est in electronics and fuel-cell applications, and stabilization at ambient conditions can be achieved by aliovalent substitution and nanosize effects. Y³⁺ stabilization of hafnia (YSH) introduces local cation disorder around charge-com­pensating oxygen-ion vacancies, and here we establish both the average and local structure of YSH nanoparticles using synchrotron powder X-ray diffraction (PXRD) and pair distribution function (PDF) analysis. A range of phase-pure crystalline nanoparticles of Hf_{1–<em>x</em>}Y_<em>x</em>O_{2–<em>x</em>/2} were prepared <em>via</em> continuous flow solvothermal synthesis and subsequent high-tem­per­a­ture annealing, and full stabilization of the cubic phase is achieved already at 13 at% Y³⁺. The average structure conforms to the cubic fluorite phase of HfO₂, but local displacive disorder caused by electrostatic attraction of neighbouring oxygen ions and repulsion of neighbouring metal ions by the net-positive oxygen-ion vacancies is established. The well-known Zr₃Y₄O₁₂ structure, which incorporates such relaxation motifs, provides a good pr­oxy description of YSH. <em>In situ</em>X-ray total scattering experiments provide insight into the formation mechanism of the YSH nanoparticles and initial precipitation of an atomically mixed amorphous phase is followed by crystallization over several minutes. The crystallization rate in­creases with higher reaction tem­per­a­ture, whereas an increased doping level results in slower crystallization.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 485-497"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148204385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The resolution revolution revisited","authors":"Edward H. Egelman","doi":"10.1107/S2052252526006123","DOIUrl":"10.1107/S2052252526006123","url":null,"abstract":"","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 304-305"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148251528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CryoEM structures reveal allosteric regulation of the catalytic activity of the multi-protein human MAT enzyme complexes","authors":"Faisal T. Khaja,&nbsp;Reedhi Vara,&nbsp;Louie P. Aspinall,&nbsp;Ciara Merriman,&nbsp;Alana Maerivoet,&nbsp;Joshua B. R. White,&nbsp;Stephen P. Muench,&nbsp;S. Samar Hasnain,&nbsp;S. V. Antonyuk","doi":"10.1107/S2052252526005075","DOIUrl":"10.1107/S2052252526005075","url":null,"abstract":"<div><div>S-Adenosyl me­thio­nine (SAMe), the biological methyl donor essential for sustaining the life of most complex organisms, is the second most widely used cofactor, after ATP, in biochemical reactions and is synthesized by the enzyme me­thio­nine adenosyl transferase (MAT) from ATP and me­thio­nine. MAT, also known as <em>S</em>-adenosylme­thio­nine synthetase, is found in almost every organism. SAMe is employed universally by different methyl­transferases that catalyze the methyl­ation of biomolecules such as nucleic acids, proteins and lipids. In plant cells SAMe produced by MAT enzymes controls the level of critical metabolites such as ethyl­ene, polyamines and biotin, and regulates essential cellular processes such as cell division and synthesis of cell wall, chloro­phyll and membrane. MAT enzyme complex MATα2β, comprising the catalytic unit MATα2 and the regulatory protein MATβ, is found in nearly all human tissues and is essential for providing the necessary SAMe flux for methyl­ation of DNA and various proteins including histones. The enzymatic activity of MATα2 is enhanced by several fold upon complexation with both variants of MATβ (βV1 and βV2). Using cryogenic electron microscopy, we determined the high-resolution resting-state structures of the MATα2₄βV1₂ and MATα2₄βV2₂ complexes, providing insights into the allosteric regulation of MAT catalytic activity, revealing how MATβV association could facilitate substrate binding, stabilize the transition state and promote product release to drive the catalytic cycle, and opening new possibilities for inhibitor binding.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 373-384"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148301704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Additive-driven microwave crystallization of tyramine polymorphs and salts: a quantum crystallography perspective. Corrigendum","authors":"Szymon Grabowski,&nbsp;Klaudia Nowakowska,&nbsp;Helena Butkiewicz,&nbsp;Anna Hoser,&nbsp;Aleksandra Wesełucha-Birczyńska,&nbsp;Tomasz Seidler,&nbsp;Paulina Moskal,&nbsp;Marlena Gryl","doi":"10.1107/S2052252526003283","DOIUrl":"10.1107/S2052252526003283","url":null,"abstract":"<div><div>Support by National Science Centre Poland under grant No. UMO-2023/51/B/ST5/02843 for the work described in the article by Grabowski <em>et al.</em>[(2025), <em>IUCrJ</em>, <strong>12</strong>, 403–416] is acknowledged.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Page 522"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147963726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards time-resolved MicroED grid preparation using mix-and-inject gas dynamic virtual nozzles","authors":"Jacob A. Summers,&nbsp;Niko W. Vlahakis,&nbsp;Kara A. Zielinski,&nbsp;Sarah Uttormark,&nbsp;Scout Fronhofer,&nbsp;Cole Dolamore,&nbsp;Mark A. Wilson,&nbsp;Lois Pollack,&nbsp;Jose A. Rodriguez,&nbsp;Peter D. Dahlberg,&nbsp;Soichi Wakatsuki","doi":"10.1107/S2052252526005129","DOIUrl":"10.1107/S2052252526005129","url":null,"abstract":"<div><div>Recent progress in gas dynamic virtual nozzle (GDVN) technologies in combination with high-brilliance synchrotron and X-ray free-electron lasers (XFELs) has allowed the visualization of protein dynamics <em>in crystallo</em> by mixing macromolecular protein crystals with a substrate using tunable mixing times on the order of milliseconds to seconds prior to serial X-ray diffraction data collection. This has become the method of choice for high-resolution structure determination of intermediate states. However, such experiments require large counts of crystals of proper sizes for high-resolution data collection, and premium beam times for screening efforts. Cryogenic microcrystal electron diffraction (MicroED) represents a complementary technique that may be a more accessible avenue for time-resolved nanocrystallography compared with serial X-ray diffraction experiments. MicroED can produce full diffraction datasets from just a few submicrometre-thick crystals, and the approach is more readily accessible, requiring standard cryogenic transmission electron microscopy (TEM) equipment available at many universities and institutes. Cryogenic MicroED, like other forms of cryo-EM, begins with rapidly freezing biological material on electron microscopy grids. In the case of MicroED, micro- to nano-crystals (&lt;500 nm thick) are deposited onto electron microscopy grids and plunge-frozen for subsequent electron diffraction data collection. Here, we have incorporated GDVN technology developed originally for XFEL experiments into the freezing process as a first step towards time-resolved studies. We describe the limited deposition efficiency of the model MicroED protein proteinase K on TEM grids using GDVNs, preceding sample vitrification and successful MicroED data collection. We discuss both the initial results from such experiments and the methodological challenges in developing this approach into a reliable workflow for millisecond-to-second time-resolved structural studies of macromolecules. Our results promise a strategy to deposit crystals on grids using GDVNs and determine high-resolution structures by MicroED, constituting a first step towards development of time-resolved MicroED experiments.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 514-521"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148301668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cryo-EM analysis of cooperative conformational changes in the SARS-CoV-2 spike protein trimer","authors":"Qiyu Wang,&nbsp;Spencer Cholak,&nbsp;Geoffrey Woollard,&nbsp;Sriram Subramaniam,&nbsp;Khanh Dao Duc","doi":"10.1107/S2052252526004513","DOIUrl":"10.1107/S2052252526004513","url":null,"abstract":"<div><div>The entry of SARS-CoV-2 into cells is mediated by a trimeric spike protein that utilizes its receptor-binding domain (RBD) to engage with the cell surface receptor ACE2, with each protomer capable of shuttling between an ‘up’ conformation that can bind ACE2 and a ‘down’ conformation that prevents ACE2 binding. To discover inter­mediate conformational states during this transition, we applied and refined a recently reported linear subspace method to embed 2D projection cryo-EM images of ACE2-bound spike proteins into a low-dimensional latent space. From this embedding, multiple conformational states were reconstructed followed by an automated masking protocol, leveraging a topology representing network and optimal transport. A surprising result from our analysis is the finding that the dominant trajectory for the transition between conformations that have one-up and two-up RBD states involves an all-down RBD conformational state. The methods we present here could be generally applicable to other dynamic protein assemblies to uncover novel inter­mediate conformational states.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 385-394"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148317201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A picture is worth a thousand diffraction spots: using photometry and computer vision to perform rapid high-throughput sample-versatile serial crystallography","authors":"Ben A. Coulson,&nbsp;Sam G. Lewis,&nbsp;Christian Orr,&nbsp;Lauren E. Hatcher,&nbsp;David R. Allan,&nbsp;Mark Warren","doi":"10.1107/S2052252526003568","DOIUrl":"10.1107/S2052252526003568","url":null,"abstract":"<div><div>The ‘photometric selection’ approach as a high throughput, sample tolerant, low cost and highly automatable method of carrying out serial crystallography is presented. Crystalline samples are loaded and distributed onto a simple transparent substrate and an in-line camera identifies crystals using image recognition algorithms from the computer vision project OpenCV. In contrast to established serial techniques, which generally require that crystal samples be refined with narrow size distributions and defined habits, the sample requirements when using photometric selection are shown to be minimal. We demonstrate how broadly effective photometric selection can be by collecting high-quality datasets from three exemplar systems: a small-mol­ecule organometallic, a small-mol­ecule organic and a metal–organic framework system. In contrast to previously established grid-scanning techniques, data collection using photometric selection can be up to six times faster.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 409-419"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147963675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cryo-EM: the revolution continues","authors":"Sriram Subramaniam,&nbsp;Werner Kühlbrandt,&nbsp;Richard Henderson","doi":"10.1107/S2052252526003842","DOIUrl":"10.1107/S2052252526003842","url":null,"abstract":"<div><div>The near-universal adoption of electron cryo-microscopy (cryo-EM) by structural and cell biologists has led to exponential growth of the field, especially over the last two decades, with a doubling in the number of deposited electron-microscopy density maps every 2.5 years. This exponential growth has changed in recent years to become linear. Cryo-EM methods are now able to contribute to our structural understanding of biological complexity ranging from atomic resolution maps of assemblies of multiprotein complexes to <em>in situ</em> investigation of protein structures in the context of intact cells, snapshots of multiple conformations and insights into fundamental chemical mechanisms underlying biological function. Combined with dramatic advances in artificial intelligence, the increasing democratization and implementation of cryo-EM appears poised to drive a new revolution in digital biology.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 306-311"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148204451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}